Rock Lee, Hinata, Shikamaru (well he did)... they were basically the "main characters" of their secondary teams. They at least should have been further developed.
Kisame, Sasori, and Kakuzu probably should have lived their battles (Sasori faking his death with the Lion thing Sakura threw... Kakuzu retreating like an experienced shinobi probably would have... Kisame actually escaping with his trick). That way they could have lead the Ambush division, Lightning Coast, and Kakuzu could have fought the second divison. Them acting as generals.
I didn't like that Akatsuki became the primary opponents of part II (should have made cameos before finally having their arcs), but they also should not have all been killed just as they appeared. Something like Itachi and Kisame's intro should have been done for each group.
Dan and the Seven Swordsmen should have all been seen fighting. Hizashi should have fought his son Neji. Kimmimaru and Chiyo should have been shown getting defeated/fighting in general.